chr10-34966173-A-G

Variant names:

• chr10-34966173-A-G
• rs2812968
• ENST00000451920.2:n.501A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000451920.2(PRDX2P2):​n.501A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 399,352 control chromosomes in the GnomAD database, including 49,002 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.52 (21276 hom., cov: 33)
  • Exomes 𝑓: 0.47 (27726 hom.)
• Consequence: PRDX2P2 ENST00000451920.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763
• Publications: 5 publications found

Genes affected

PRDX2P2 (HGNC:44967): (peroxiredoxin 2 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDX2P2		n.34966173A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDX2P2	ENST00000451920.2	n.501A>G		non_coding_transcript_exon_variant	Exon 3 of 3	6

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78293 AN: 151992 Hom.: 21234 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.483

GnomAD4 exome AF: 0.468 AC: 115680 AN: 247242 Hom.: 27726 Cov.: 0 AF XY: 0.464 AC XY: 66097 AN XY: 142522

African (AFR) AF: 0.700 AC: 4300 AN: 6146

American (AMR) AF: 0.517 AC: 9813 AN: 18976

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 2188 AN: 5418

East Asian (EAS) AF: 0.635 AC: 6274 AN: 9874

South Asian (SAS) AF: 0.487 AC: 19611 AN: 40298

European-Finnish (FIN) AF: 0.483 AC: 10090 AN: 20910

Middle Eastern (MID) AF: 0.442 AC: 341 AN: 772

European-Non Finnish (NFE) AF: 0.432 AC: 57576 AN: 133224

Other (OTH) AF: 0.472 AC: 5487 AN: 11624

GnomAD4 genome AF: 0.515 AC: 78385 AN: 152110 Hom.: 21276 Cov.: 33 AF XY: 0.516 AC XY: 38386 AN XY: 74342

African (AFR) AF: 0.684 AC: 28389 AN: 41506

American (AMR) AF: 0.484 AC: 7390 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1352 AN: 3472

East Asian (EAS) AF: 0.640 AC: 3307 AN: 5166

South Asian (SAS) AF: 0.511 AC: 2465 AN: 4822

European-Finnish (FIN) AF: 0.476 AC: 5029 AN: 10562

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29024 AN: 67982

Other (OTH) AF: 0.489 AC: 1032 AN: 2112

Alfa AF: 0.483 Hom.: 6829

Bravo AF: 0.525

Asia WGS AF: 0.617 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	1.7
DANN	Benign	0.33
PhyloP100		0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2812968; hg19: chr10-35255101;